BIOCHEMISTRY FOR THE TEACHER - F.F. BOYECHKO - 1985

ENERGETICS OF BIOLOGICAL PROCESSES

METABOLISM AND ENERGY — THE FUNDAMENTAL CHARACTERISTIC OF LIVING SYSTEMS

The most defining characteristic of living organisms is METABOLISM. Throughout their lives, all organisms continuously take up nutrients from the environment and return Metabolic waste products back into it.

The component of overall metabolism that encompasses the uptake, transformation, and assimilation of environmental substances, thereby building the Structural components of the Organism, is known as assimilation, or anabolism. A crucial feature of assimilation is that nutrients and food components—which originate as non-living matter—are transformed within the organism into living matter. The primary function of assimilation is plastic function, ensuring the continuous regeneration of the constituent parts of living systems.

All synthetic reactions within the organism require energy input. The principal source of this energy is ATP along with other high-energy compounds.

Simultaneously with assimilation, opposing processes occur within the organism—dissimilation, which involves The breakdown of complex substances into simpler ones, their subsequent transformation, and elimination into the environment as metabolic end products.

The Biological Significance of dissimilation lies in supplying the organism with energy, as the breakdown of complex molecules into simpler ones is accompanied by the release of energy.

Thus, metabolism represents a dialectical unity of two opposing processes—assimilation and dissimilation, namely Nutrition and excretion, Synthesis and degradation, buildup and breakdown. All Chemical Reactions occurring within cellular environments exhibit a high degree of Organization and regulation. Each reaction takes place at a precise cellular Location and in a specific sequence, mediated by the catalytic action of corresponding Enzymes.

Metabolism underpins all manifestations of life, including growth, reproduction, locomotion, irritability, the Maintenance of the internal environment (Homeostasis), and adaptation to various environmental conditions.

Metabolic processes are under the constant control of the Central Nervous system. As I.P. Pavlov defined it, The Nervous System acts as the master regulator of all bodily activity.

The interaction between the organism and the external environment mediated by the central nervous system can be illustrated by the following diagram (after V.I. Dobrynina):

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Metabolism encompasses A wide variety of processes occurring within the living organism, including physiological ones (such as nutrition and excretion), physical ones (such as sorption and substance transport), and chemical ones (such as decomposition, synthesis, and others). That part of metabolism driven by chemical reactions—which govern the Transformation of substances through Biosynthesis and breakdown pathways—is referred to as Intermediary Metabolism.

This metabolic network comprises hundreds of distinct, interconnected enzymatic reactions, where the products of one reaction serve as the substrate for the next. Consequently, cellular enzymatic reactions function as a cooperative, spatially and temporally organized, single multi-step process. Furthermore, The sequence of such metabolic processes is remarkably similar across all living systems, particularly regarding their central metabolic pathways.

During intermediary Catabolism, high-molecular-weight nutrients in animal organisms undergo three main stages. In The First stage, the major components of food—Proteins, Nucleic Acids, Lipids, and CARBOHYDRATES—are broken down via Hydrolysis into relatively low-molecular-weight building blocks. Specifically, proteins are cleaved into Amino Acids, nucleic acids into NUCLEOTIDES, lipids into Fatty acids, glycerol, and other constituent parts, and Polysaccharides into Monosaccharides. This process primarily takes place in the gastrointestinal tract. However, the Breakdown of Proteins, nucleic acids, fats, and carbohydrates that make up various Organ and tissue structures can also occur intracellularly.

In the second stage, the products formed During the first stage are converted into simpler molecules through anaerobic oxidation. For instance, fatty acids, glycerol, and monosaccharides are broken down into acetyl-CoA, while Amino Acids and nucleotides are converted into a variety of Other Compounds.

In the Third Stage, the compounds generated in the Second Stage undergo aerobic oxidation to yield carbon dioxide and Water. This final, shared stage of aerobic transformation is The Tricarboxylic Acid Cycle, which is closely coupled with tissue Respiration processes.

Assimilation processes are characterized by three stages. The third stage of dissimilation actually serves as the first stage of assimilation. For example, $\alpha$-keto acids are used for Protein Synthesis, while acetyl-CoA and carbon dioxide ($ ext{CO}_2$) are utilized for the synthesis of Fatty Acids and simple carbohydrates. During the second stage of assimilation, precursor compounds are converted into amino acids, fatty acids, monosaccharides, and other substances. In the third stage, these substances are further transformed into proteins, lipids, carbohydrates, and other compounds vital to the organism.

Although assimilation and dissimilation occur simultaneously within Cells and enzymes possess reversible catalytic activity, their metabolic pathways do not coincide. The enzyme systems that catalyze assimilation and dissimilation are localized in different cellular compartments. Furthermore, these processes feature distinct regulatory mechanisms.

All metabolic processes in the living organism are inextricably linked with Energy Metabolism and transformation. It is well known that nutrients entering the body with food possess a certain reserve of potential energy. But where does the initial energy originate, serving as the essential source of life on Earth?

The answer to this question was provided in the works of K. A. Timiryazev.

K. A. Timiryazev's research demonstrated that light energy is absorbed by chlorophyll and channeled into driving chemical reactions driven by the synthesis of organic matter. Under these conditions, the transformed solar Energy is stored as potential energy, commonly referred to as Free energy. It is concentrated within the chemical bonds between atoms of various Organic compounds. During dissimilation, energy is released and partially utilized in assimilation processes—namely, in The formation of chemical compounds necessary for body Structure and vital activity. Consequently, The amount of free energy contained within the molecules of organic compounds changes during their transformation.

If The change in free energy within compounds resulting from the Cleavage or formation of a chemical bond amounts to 12—17 kJ/mol, they are classified as standard energy compounds. However, A number of compounds are known where the change in free energy upon chemical bond cleavage equals 20 kJ/mol or more. Such compounds are termed high-energy (macroergic) compounds, and the bonds whose transformations account for these shifts in the Energy balance are called high-energy bonds, conventionally denoted by the symbol ~ (tilde).

The energy released during the cleavage of high-energy bonds is absorbed during the synthesis of organic compounds. The body's reserves of high-energy compounds are continuously replenished through the accumulation of energy released when substances undergoing breakdown drop to a lower energy level. Thus, high-energy compounds function as both Donors and acceptors of energy in metabolism.

The main macroergic compounds of the organism are ATP, phosphoenolpyruvate, 1,3-diphosphoglyceric acid, creatine phosphate, acetyl phosphate, etc.

ATP occupies a central place in energy metabolism. It has The ability to store energy and release it as needed during metabolic processes. ATP also Functions as a carrier of energy-rich phosphate groups from high-energy phosphorylated compounds that are thermodynamically positioned above it to less energy-rich compounds, which become activated upon receiving a phosphate. ATP plays a crucial role in the metabolism of macroergic compounds themselves. The synthesis of a number of nucleotide triphosphates—GTP, UTP, TTP, and CTP—occurs with the participation of ATP. The energy of ATP is utilized in the body for a wide variety of processes.

Thus, the processes of matter and energy exchange are interconnected and form The basis of the vital activity of organisms.

Biological Oxidation

Biological oxidation processes are the primary source of energy in the organism.

The foundations of The Theory of oxidation were originally developed by M. V. Lomonosov and A. Lavoisier while investigating combustion processes. All Reactions Involving the addition of oxygen to any substance came to be called oxidation, while the removal of oxygen processes were termed reduction.

Comparing combustion processes with animal respiration, A. Lavoisier noted that they share much in common. During respiration, as in combustion, oxygen is absorbed from the air, and CO₂ and H₂O are formed. The energy yield resulting from The oxidation of organic substances (e.g., glucose) inside and outside the body also proved to be identical.

However, it remained unclear why the combustion of substances in the body occurs at a low Temperature (37°C), without a flame, and furthermore in an aqueous environment.

Several theories were proposed to explain The process of substance oxidation in the body. Among them, the theory of Academician A. M. Bakh was of particular importance. He proved that the oxidation of organic substances in the body by molecular oxygen occurs with the formation of peroxides, which play a crucial role in oxygen activation. Such substances include unsaturated compounds—lipolic, linolenic, and arachidonic acids, carotenes, vitamin A, Terpenes, etc. They readily interact with molecular oxygen to form peroxides, which, with the participation of peroxidase enzymes, break down to form active oxygen. The latter has the ability to oxidize other molecules of organic compounds that do not react with molecular oxygen:

Since the oxidation of substances occurs with the formation of peroxides, A. M. Bakh's theory became known as the peroxide theory.

A significant contribution to the understanding of biological oxidation processes was made by the Soviet biochemist V. I. Palladin. He established that the oxidation of substances in plants can also occur in the absence of oxygen, provided that substances capable of binding hydrogen are present in the reaction medium. These substances turned out to be pigments—chromogens. By binding hydrogen from the substrates undergoing oxidation, they are reduced and become colorless; then they release it (i.e., become oxidized) and regain their color, transforming into Quinones. This transformation takes place with the participation of atmospheric oxygen:

It should be noted that V. I. Palladin attached great importance to oxygen as a hydrogen acceptor, thereby revealing the vital role of oxygen in biological oxidation processes. V. I. Palladin's research was confirmed by the German scientist Wieland. He expressed the view that the dehydrogenation of substrates is the fundamental process underlying biological oxidation, and that oxygen reacts with already activated hydrogen atoms. Thus, the theory of substance oxidation via dehydrogenation was formulated, which became known as the Palladin-Wieland theory.

Confirmation of this theory came from the discovery and study of a number of dehydrogenases—enzymes that catalyze the removal of hydrogen atoms from various substrates. At the same time, it was proven that substrate oxidation processes represent a chain of successive reactions beginning with the dehydrogenation of substrates and ending with The transfer of electrons to oxygen and the interaction of the latter with hydrogen protons to form water. Since such oxidation is accompanied by a continuous uptake of oxygen, it is also referred to as cellular respiration.

Thus, based on M. O. Bakh's peroxide theory, the Palladin-Wieland theory of substrate dehydrogenation, and subsequent research, modern concepts regarding The Mechanism of biological oxidation were established.

MODERN CONCEPTS OF Biological Oxidation

The process of biological oxidation occurs in stages. It involves enzyme systems containing NAD+, NADP+, FMN, FAD, ubiquinones, and iron-porphyrin complexes as their non-protein moieties.

At the first stage of biological oxidation, the dehydrogenation of substrates—breakdown products of proteins, fats, and carbohydrates—takes place with the participation of dehydrogenase enzymes (oxidoreductases) containing NAD+ and NADP⁺ Coenzymes. They serve as nearly universal hydrogen acceptors for a range of substrates, including alcohols, aldehydes, dicarboxylic and keto acids, amines, etc. By abstracting hydrogen atoms from substrates, dehydrogenases are reduced while the substrates are oxidized:

As can be seen from the scheme, the functional group of dehydrogenases is nicotinic acid amide. The hydrogen atoms split off from the substrate attach to the carbon at the fourth position of the nicotinamide ring. From the second hydrogen atom of the substrate, an electron attaches to the nitrogen at the first position, neutralizing its positive charge, while a proton passes into the solution.

An example of dehydrogenases is Lactate dehydrogenase, which catalyzes the dehydrogenation reaction of lactic acid:

It should be noted that the reaction Specificity of this group of dehydrogenases is determined by the protein part of the enzyme, since their coenzymes are identical in structure.

At the next stage of biological oxidation, the hydrogen atom acceptor is a group of flavin enzymes that contain FMN and FAD as their non-protein prosthetic groups. They mediate the transfer of hydrogen atoms from reduced NAD or NADP. This process can be illustrated by the following scheme:

Next, electrons and protons are transferred from the reduced forms of FMN or FAD to ubiquinones (coenzyme Q, see p. 219).

At the subsequent stage, protons from coenzyme Q are released into the surrounding medium, while electrons are transferred to the cytochrome system. The cytochrome system consists of a series of oxidoreductases whose non-protein moiety is represented by iron-Porphyrins, structurally similar to heme. More than 20 different Cytochromes are currently known. They are designated by the corresponding Latin letters — a, b, c, d, etc. The cytochrome system includes cytochromes and an enzyme known as cytochrome oxidase. A characteristic feature of this enzyme system is that they transfer electrons from reduced coenzyme Q to oxygen, which then combines with ionized hydrogen atoms to form water:

As seen from the presented scheme, the process of electron transfer through the cytochrome system is accompanied by A change in the valence of the iron atom within the porphyrin ring. In oxidized cytochromes, Fe³⁺ accepts electrons and is converted into Fe²+. From the final cytochrome, electrons are transferred to cytochrome oxidase, which is subsequently oxidized directly by oxygen. In the course of cellular respiration, In addition to water, carbon dioxide (IV) is formed, and energy is released and stored in the form of ATP.

This chain of oxidation-reduction processes creates a distinctive electronic cascade. At various segments of this cascade, differing amounts of energy are released, which is quantified by the redox potential. For a significant portion of substrates, the Redox Potential of the redox systems ranges around 0,6 V. The redox potential determines the direction of electron transfer along the Respiratory Chain. There is a progressive increase in the redox potential from the first stage to the last (Table 12).

Table 12. Values of standard redox potentials E₀ of the Main Components of the redox chain

(at pH 7 and T 38 °C)

Note: The redox potential value is expressed in terms of electromotive force — E₀.

Other pathways of tissue respiration—both longer and shorter—are also known. An example of a long tissue respiration chain is the oxidation of α-keto acids. During The oxidative decarboxylation of these acids, two hydrogen atoms are first transferred to Lipoic Acid and subsequently to nicotinamide coenzymes. A shorter pathway is involved in the oxidation of succinic acid to fumaric acid. In this process, two hydrogen atoms bypass the nicotinamide coenzymes and are transferred directly to flavin enzymes.

Oxidative Phosphorylation

It has been proven that during biological oxidation, over 50 % of the released energy is conserved by tissue cells in the form of high-energy compounds, predominantly as

ATP. ATP is synthesized with the participation of ADP and activated inorganic phosphate. The activation of the latter occurs primarily at the expense of energy derived from biological oxidation. Consequently, Oxidative phosphorylation is the phosphorylation of ADP coupled with oxidation processes in the body, which is accompanied by the formation of ATP.

Oxidative phosphorylation was first discovered by V. O. Engelhardt in 1930. Somewhat later, in 1939, V. O. Belitzer and co-workers established the relationship between electron transfer processes in the Cell/36.html">Respiratory Chain and phosphorylation. The P/O ratio (The ratio of phosphorylation to oxidation) was also investigated. A significant contribution to elucidating the Mechanism of Oxidative phosphorylation was made by S. E. Severin, V. P. Skulachev, P. Mitchell, and other domestic and foreign researchers.

Oxidative phosphorylation occurs primarily within Mitochondria. The enzymes catalyzing this process are localized in the mitochondrial membranes. Mitochondria are the most vital cellular Organelles that generate energy through the Oxidation of proteins, fats, carbohydrates, and other organic compounds. Therefore, they are often referred to as the "power plants" of The Cell.

It has been established that there are three sites in the respiratory chain where ATP synthesis takes place:

As can be seen from the presented scheme, the first ATP molecule is synthesized As a result of electron and proton transfer from nicotinamide to Flavin Coenzymes, the second—during Electron transfer from cytochrome b to cytochrome c. And finally, the third ATP molecule is formed at the site of electron transfer from cytochrome oxidase (a₃) to oxygen. Thus, the oxidation of two hydrogen atoms in the respiratory chain yields three molecules of ATP.

The intensity of oxidative phosphorylation is regulated by the ATP/ADP ratio. The lower this ratio, the more intensive the respiration process and ATP formation become.

Currently, several hypotheses exist to explain the mechanism of oxidative phosphorylation.

The Essence of the chemical hypothesis is that the energy released during electron transfer in the respiratory chain is initially utilized to form certain hypothetical high-energy compounds. From these compounds, the energy is subsequently transferred to drive the synthesis of ATP. This process can be schematically represented as follows:

where A and B are electron-carrying substances; P_i is inorganic phosphate; X is an unknown, hypothetical substance.

The chemiosmotic hypothesis was proposed by Peter Mitchell and was experimentally substantiated and further developed in the research of V. P. Skulachev. Its core premise is that the chemical energy of oxidation is converted into electrical potentials across the outer and inner surfaces of the mitochondrial membrane. The difference between these potentials serves as the energy source driving ATP synthesis. Compared to other hypotheses, this one is the most thoroughly substantiated, although it still leaves several unresolved questions that require further investigation.

In addition to Oxidation coupled with phosphorylation, the body can undergo tissue respiration that is not accompanied by phosphorylation—meaning it does not result in ATP formation. This type of oxidation is referred to as non-phosphorylating or Free Oxidation. Although this form of biological oxidation also takes place in the mitochondria, the energy released in the process is dissipated as heat. Free oxidation plays a vital role in organismal adaptation to various adverse environmental conditions. Specifically, research has shown that upon bodily cooling, phosphorylation-coupled respiration decreases, whereas free oxidation increases to help maintain core body temperature.

The body employs a number of mechanisms capable of altering the balance between OXIDATIVE PHOSPHORYLATION AND free oxidation. For instance, the hormone thyroxine uncouples oxidation from phosphorylation, whereas Insulin has the opposite effect, strengthening this coupling. A variety of other compounds—such as dinitrophenol, dicoumarol, aspirin, and phenacetin—are also known to inhibit the Coupling of oxidation and phosphorylation processes. These substances are commonly referred to as uncoupling agents (factors).